PR: OPSIN verification by default in the CLI + Readme fix #68
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| name: CI | |
| on: | |
| push: | |
| branches: [main, refactor_namer] | |
| pull_request: | |
| branches: ["**"] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install ruff | |
| run: pip install "ruff==0.15.15" | |
| - name: Ruff check | |
| run: ruff check src/bluenamer | |
| - name: Ruff format check | |
| run: ruff format --check src/bluenamer | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| - name: Set up JDK (for OPSIN) | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: temurin | |
| java-version: "17" | |
| - name: Install package | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[dev]" | |
| - name: Run fast tests | |
| run: | | |
| pytest -m "not slow and not dataset and not golden" \ | |
| --maxfail=20 \ | |
| --durations=20 | |
| rdkit-compat: | |
| # Strict golden-output regression across RDKit versions. Detects | |
| # naming output that drifts with the RDKit upgrade cycle (aromaticity, | |
| # kekulisation, H-count perception). Each matrix row pins a specific | |
| # rdkit and runs only the `golden` test. | |
| runs-on: ubuntu-latest | |
| needs: [lint] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| rdkit-version: | |
| - "2024.03.6" | |
| - "2024.09.6" | |
| - "2025.03.6" | |
| - "2025.09.5" | |
| - "2026.3.2" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: pip | |
| - name: Install package + pinned rdkit | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[dev]" | |
| pip install --force-reinstall --no-deps "rdkit==${{ matrix.rdkit-version }}" | |
| - name: Show installed versions | |
| run: | | |
| python -c "import rdkit, sys; print('python', sys.version); print('rdkit', rdkit.__version__)" | |
| - name: Run golden corpus test | |
| run: pytest -m golden -v --no-header -rA | |
| docker: | |
| runs-on: ubuntu-latest | |
| needs: [lint] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/setup-buildx-action@v3 | |
| - name: Build image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| push: false | |
| load: true | |
| tags: bluenamer:ci | |
| - name: Smoke-test the image | |
| run: | | |
| docker run -d --name bluenamer-ci -p 8000:8000 bluenamer:ci | |
| for i in $(seq 1 30); do | |
| if curl -fsS http://127.0.0.1:8000/healthz > /tmp/health.json; then | |
| cat /tmp/health.json | |
| exit 0 | |
| fi | |
| sleep 2 | |
| done | |
| docker logs bluenamer-ci | |
| exit 1 |